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Unable to install OHDSI in Mac OS Mojave

General
#1

I am trying to install OHDSI in Mac OS Mojave with dart.

install.packages(“drat”)
drat::addRepo(“OHDSI”)
install.packages(“PatientLevelPrediction”)

I recive the following errors,

install.packages(“PatientLevelPrediction”)
Installing package into ‘/Users/u0979082/packrat/lib/x86_64-apple-darwin15.6.0/3.6.1’
(as ‘lib’ is unspecified)
Warning in install.packages :
unable to access index for repository https://OHDSI.github.io/drat/bin/macosx/el-capitan/contrib/3.6:
cannot open URL ‘https://OHDSI.github.io/drat/bin/macosx/el-capitan/contrib/3.6/PACKAGES’

package ‘PatientLevelPrediction’ is available as a source package but not as a binary

Warning in install.packages :
package ‘PatientLevelPrediction’ is not available (as a binary package for R version 3.6.1)

I have R Studio : Version 1.2.5001 and R version 3.6.1.

Since this method did not work I also tried to install using devtools. However, I get the following errors when I tried to install SqlRender.

install_github(“ohdsi/SqlRender”)
Downloading GitHub repo ohdsi/SqlRender@master
:heavy_check_mark: checking for file ‘/private/var/folders/22/pz8hk02x2hj985j4klbz5gkm0000gp/T/Rtmp6OoEMP/remotes473a48b130ca/OHDSI-SqlRender-2fc4405/DESCRIPTION’ …
Error in system2(“cp”, “–version”, stdout = TRUE, stderr = FALSE) :
error in running command
Execution halted
sh: rm: command not found
Error: Failed to install ‘SqlRender’ from GitHub:
System command error, exit status: 1, stdout + stderr:
E> * checking for file ‘/private/var/folders/22/pz8hk02x2hj985j4klbz5gkm0000gp/T/Rtmp6OoEMP/remotes473a48b130ca/OHDSI-SqlRender-2fc4405/DESCRIPTION’ … OK
E> Error in system2(“cp”, “–version”, stdout = TRUE, stderr = FALSE) :
E> error in running command
E> Execution halted
E> sh: rm: command not found

According to some forums, this is a sign that I do not have XCode. However, in my case I have XCode already installed.
“xcode-select --install
xcode-select: error: command line tools are already installed, use “Software Update” to install updates”

I greatly appreciate if anybody could help me with this issue.

#2

Wondering whether this is a question no body knows the answer.

#3

@jreps - as you have a Mac, do you see these issues when installing SqlRender locally?

#4

I managed to get everything installed on my Mac. I think I did have some Xcode issue when I wanted to build packages but I think I just installed Xcode and set any necessary environmental variables. R doesn’t update the settings until you close and restart R, so if you set up Xcode during the R session you might still see the issue until you close and restart. If you installed Xcode ages ago maybe try updating it and see whether that fixes things?

#5

I had a problem before I installed XCode in Mac. So as @jreps said, install XCode first. I think this solve the problem.

If you cannot solve this problem anyway, docker can be another solution.

#6

Hi @SCYou

Docker would be a great solution. I have the docker container running. However, I am not sure how to run the patientlevelprediction in R Studio. Could you please point me to a place where I could find how to run the model with the docker.

#7

@Ajith_Lindhe

Locally means download first and then install?

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